Hydrogen bond number

[chenyu zhang]

Dear Professor:

  I read your article "Calculation of 1D and 2D densities in VMD: A flexible and easy-to-use code". I would like to ask you three questions: 

  1. If the system is not a cuboid but a periodic parallelepiped, is this code still applicable and how should it be modified? 

  2. If the solution is an acidic aqueous solution or an alkaline aqueous solution containing protons or hydroxides, how should atomSelection be selected in the code? 

  3. Also, does this code give the number of hydrogen bonds?

  Look forward to your answer, thank you professor!

  Yours sincerely.

[Y. Wang]

Dear Chenyu,

Thank you for using the code.

For your questions, here are my comments.

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  1. If the system is not a cuboid but a periodic parallelepiped, is this code still applicable and how should it be modified?

Comment: The code doesn’t matter what shape the system is, but the parameter “cell” does. If your concerned area is not a cuboid, you can set a cuboid cell which is larger than your concerned area, the code can still calculate the HB, but with some vacuum area. In your case, the periodic parallelepiped, I may suggest you slice your system into several cuboids, then calculate the HB in each cuboid.

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  2. If the solution is an acidic aqueous solution or an alkaline aqueous solution containing protons or hydroxides, how should atomSelection be selected in the code?

Comment: You asked a very good question. The method that the code calculating HB is based on VMD command “measure hbonds”, this command requires the donor bonded to a hydrogen atom (VMD can determine if the hydrogen atom is bonded to a donor or not by distance), if not, the hydrogen atom cannot by involved into a HB. But hydroxides should be OK since all atoms in a hydroxide are bonded. You can involve all atom names or types into the parameter “atomSelection”, for example, {name O1 O2 O3 H1 H2 H3}, or use other VMD atom selection syntax to include your concerned atoms or molecules, please refer to the VMD user guide, or if you can read Chinese, please see this link: http://sobereva.com/504

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  3. Also, does this code give the number of hydrogen bonds?

Comment: Of course the code can tell the total number of HBs in each frame, this information is stored in hbNumRecord.dat.

Hope these comments help you. If you still have concerns, please feel free to respond to this reply. Thank you! 

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